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MCL coexpression mm9:1421: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!4.73e-09!51
|ontology_enrichment_uberon=UBERON:0007023!4.73e-09!51
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.346849,1.35778,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,0.692139,0.6581,0.955327,0,0.856992,0.338549,0.232269,0.143775,0.426133,0.35122,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.589948,0.364821,0.607065,0.326478,0.629145,0.303703,0.752287,0.342638,0.56353,0.327433,0.959963,0.368882,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,1.69993,0.174327,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,0.11437,1.156,0.208101,0.19692,0.204132,0.763395,0.922432,0.430551,0.708505,0.874787,0.722675,0.240896,1.03903,0.439832,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.9304,0.2995,0.769162,0.244935,0.976308,0.775372,0.483322,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,1.10269,0.605144,1.33732,0.340765,0.528609,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.540361,1.10885,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,1.52669,0.30995
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.346849,1.35778,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,0.692139,0.6581,0.955327,0,0.856992,0.338549,0.232269,0.143775,0.426133,0.35122,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.589948,0.364821,0.607065,0.326478,0.629145,0.303703,0.752287,0.342638,0.56353,0.327433,0.959963,0.368882,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,1.69993,0.174327,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,0.11437,1.156,0.208101,0.19692,0.204132,0.763395,0.922432,0.430551,0.708505,0.874787,0.722675,0.240896,1.03903,0.439832,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.9304,0.2995,0.769162,0.244935,0.976308,0.775372,0.483322,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,1.10269,0.605144,1.33732,0.340765,0.528609,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.540361,1.10885,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,1.52669,0.30995
|tfbs_overrepresentation_jaspar=MA0003.1;0.276983,MA0004.1;1.3269,MA0006.1;0.945134,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.0315641,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.969171,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;1.64201,MA0040.1;1.00009,MA0041.1;1.15799,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.486223,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.212634,MA0056.1;0,MA0057.1;0.149949,MA0058.1;1.94869,MA0059.1;0.449345,MA0060.1;2.1282,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.00140584,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.358337,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;1.75322,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;1.16089,MA0103.1;0.398766,MA0105.1;0.57901,MA0106.1;0.737893,MA0107.1;1.0169,MA0108.2;0.824407,MA0109.1;0,MA0111.1;1.2824,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.119202,MA0146.1;0.990842,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.591842,MA0035.2;0.630778,MA0039.2;0.00481054,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;2.05302,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.763394,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;2.13869,MA0155.1;0.132921,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.0465447,MA0163.1;0.0423021,MA0164.1;1.58466,MA0080.2;1.01893,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.00464563,MA0102.2;1.7182,MA0258.1;0.790457,MA0259.1;0.833237,MA0442.1;0
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Revision as of 13:18, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:61216675..61216726,-p1@ENSMUST00000122927
p1@ENSMUST00000127117
p1@ENSMUST00000143264
p1@uc008icf.2
p1@uc008icg.2
p1@uc008ici.1
Mm9::chr4:62021470..62021545,-p1@Fkbp15
Mm9::chr4:73897832..73897894,+p1@Kdm4c
Mm9::chr5:110295720..110295766,+p@chr5:110295720..110295766
+
Mm9::chr8:93593951..93594022,+p1@Rbl2
Mm9::chrX:20639107..20639188,-p1@Zfp182


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0016568chromatin modification0.0278390932588522
GO:0006325establishment and/or maintenance of chromatin architecture0.0278390932588522
GO:0006323DNA packaging0.0278390932588522
GO:0051276chromosome organization and biogenesis0.0278390932588522
GO:0030426growth cone0.0278390932588522
GO:0030427site of polarized growth0.0278390932588522
GO:0006355regulation of transcription, DNA-dependent0.0278390932588522
GO:0006351transcription, DNA-dependent0.0278390932588522
GO:0032774RNA biosynthetic process0.0278390932588522
GO:0003677DNA binding0.0278390932588522
GO:0045449regulation of transcription0.0278390932588522
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0278390932588522
GO:0006350transcription0.0278390932588522
GO:0010468regulation of gene expression0.0278390932588522
GO:0005884actin filament0.0278390932588522
GO:0031323regulation of cellular metabolic process0.0281658112945624
GO:0019222regulation of metabolic process0.0284271100944954
GO:0006259DNA metabolic process0.0284271100944954
GO:0016070RNA metabolic process0.0284271100944954
GO:0043170macromolecule metabolic process0.0300812145158244
GO:0010467gene expression0.0400737164773372
GO:0003676nucleic acid binding0.0400737164773372
GO:0044238primary metabolic process0.0400737164773372
GO:0051213dioxygenase activity0.0400737164773372
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0400737164773372
GO:0044237cellular metabolic process0.0400737164773372
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0400737164773372
GO:0030424axon0.0400737164773372
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0415391950259398
GO:0050794regulation of cellular process0.0490363897477721



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism4.73e-0951


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.10.276983
MA0004.11.3269
MA0006.10.945134
MA0007.10.52077
MA0009.10.987341
MA0014.10.0315641
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.969171
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.11.64201
MA0040.11.00009
MA0041.11.15799
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.212634
MA0056.10
MA0057.10.149949
MA0058.11.94869
MA0059.10.449345
MA0060.12.1282
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.00140584
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.11.75322
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.11.16089
MA0103.10.398766
MA0105.10.57901
MA0106.10.737893
MA0107.11.0169
MA0108.20.824407
MA0109.10
MA0111.11.2824
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.10.990842
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.591842
MA0035.20.630778
MA0039.20.00481054
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.22.05302
MA0047.20.685741
MA0112.20.119197
MA0065.20.763394
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.12.13869
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.0465447
MA0163.10.0423021
MA0164.11.58466
MA0080.21.01893
MA0018.20.669032
MA0099.20.781628
MA0079.20.00464563
MA0102.21.7182
MA0258.10.790457
MA0259.10.833237
MA0442.10
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